return 0;
}
+int set_potential2b_post(t_moldyn *moldyn,pf_func2b_post func,void *params) {
+
+ moldyn->func2b=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
moldyn->func3b=func;
!(jtom->attr&ATOM_ATTR_3BP))
continue;
- /*
- * according to mr. nordlund, we dont need to take the
- * sum over all atoms now, as 'this is centered' around
- * atom i ...
- * i am not quite sure though! there is a not vanishing
- * part even if f_c_ik is zero ...
- * this analytical potentials suck!
- * switching from mc to md to dft soon!
- */
+ /* neighbourhood of atom j is not needed! */
// link_cell_neighbour_index(moldyn,
// (jtom->r.x+moldyn->dim.x/2)/lc->x,
if(ktom==&(itom[i]))
continue;
-printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+//printf("Debug: atom %d before 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
moldyn->func3b(moldyn,&(itom[i]),jtom,ktom,bc_ijk);
-printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
+//printf("Debug: atom %d after 3bp: %08x %08x %08x | %.15f %.15f %.15f\n",i,&itom[i],jtom,ktom,itom[i].r.x,itom[i].f.x,itom[i].v.x);
} while(list_next(that)!=\
L_NO_NEXT_ELEMENT);
/* 2bp post function */
if(moldyn->func2b_post)
- mlodyn->func2b_post(moldyn,
+ moldyn->func2b_post(moldyn,
&(itom[i]),
jtom,bc_ij);
exchange->h=&(params->h[num]);
exchange->betan=pow(*(exchange->beta),*(exchange->n));
+ exchange->n_betan=*(exchange->n)*exchange->betan;
exchange->c2=params->c[num]*params->c[num];
exchange->d2=params->d[num]*params->d[num];
exchange->c2d2=exchange->c2/exchange->d2;
exchange=&(params->exchange);
exchange->run3bp=0;
+ exchange->run2bp_post=0;
/*
* we need: f_c, df_c, f_r, df_r
f_r=A*exp(-lambda*d_ij);
df_r=-lambda*f_r/d_ij;
- /* f_a, df_a calc + save for 3bp use */
+ /* f_a, df_a calc + save for later use */
exchange->f_a=-B*exp(-mu*d_ij);
exchange->df_a=-mu*exchange->f_a/d_ij;
exchange->f_c=f_c;
exchange->df_c=df_c;
- /* enable the run of 3bp function */
+ /* enable the run of 3bp function and 2bp post processing */
exchange->run3bp=1;
+ exchange->run2bp_post=1;
/* reset 3bp sums */
- exchange->3bp_sum1=0.0;
- exchange->3bp_sum2=0.0;
+ exchange->sum1_3bp=0.0;
+ exchange->sum2_3bp=0.0;
+ v3_zero(&(exchange->db_ij));
return 0;
}
/* tersoff 2 body post part */
-int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
/* here we have to allow for the 3bp sums */
t_tersoff_mult_params *params;
t_tersoff_exchange *exchange;
- t_3dvec force,temp,*db_ij;
+ t_3dvec force,temp,*db_ij,*dist_ij;
double db_ij_scale1,db_ij_scale2;
double b_ij;
double f_c,df_c,f_a,df_a;
+ double chi,betan;
+ double help;
+ double n;
params=moldyn->pot2b_params;
- exchange=&(moldyn->exchange);
+ exchange=&(params->exchange);
+
+ /* we do not run if f_c_ij was dtected to be 0! */
+ if(!(exchange->run2bp_post))
+ return 0;
db_ij=&(exchange->db_ij);
f_c=exchange->f_c;
df_c=exchange->df_c;
f_a=exchange->f_a;
df_a=exchange->df_a;
+ betan=exchange->betan;
+ n=*(exchange->n);
+ chi=exchange->chi;
+ dist_ij=&(exchange->dist_ij);
- db_ij_scale1=(1+betan*3bp_sum1);
- db_ij_scale2=(n*betan*3bp_sum2);
+ db_ij_scale1=(1+betan*exchange->sum1_3bp);
+ db_ij_scale2=(exchange->n_betan*exchange->sum2_3bp);
help=pow(db_ij_scale1,-1.0/(2*n)-1);
b_ij=chi*db_ij_scale1*help;
db_ij_scale1=-chi/(2*n)*help;
+ /* db_ij part */
v3_scale(db_ij,db_ij,(db_ij_scale1*db_ij_scale2));
v3_scale(db_ij,db_ij,f_a);
+ /* df_a part */
v3_scale(&temp,dist_ij,b_ij*df_a);
+ /* db_ij + df_a part */
v3_add(&force,&temp,db_ij);
v3_scale(&force,&force,f_c);
- v3_scale(&temp,&dist_ij,f_a*b_ij*df_c);
+ /* df_c part */
+ v3_scale(&temp,dist_ij,f_a*b_ij*df_c);
/* add energy of 3bp sum */
moldyn->energy+=(0.5*f_c*b_ij*f_a);
- /* add force of 3bp calculation */
+
+ /* add force of 3bp calculation (all three parts) */
v3_add(&(ai->f),&temp,&force);
return 0;
t_3dvec temp,force;
double R,S,s_r;
double d_ij,d_ij2,d_ik,d_jk;
- double f_c,df_c,b_ij,f_a,df_a;
+ double f_c,df_c,f_a,df_a;
double f_c_ik,df_c_ik,arg;
- double scale;
- double chi;
- double n,c,d,h,beta,betan;
+ double n,c,d,h;
double c2,d2,c2d2;
double numer,denom;
double theta,cos_theta,sin_theta;
double d_theta,d_theta1,d_theta2;
- double h_cos,h_cos2,d2_h_cos2;
- double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
- double bracket3,bracket3_pow_1,bracket3_pow;
+ double h_cos,d2_h_cos2;
+ double frac,bracket,bracket_n_1,bracket_n;
+ double g;
int num;
params=moldyn->pot3b_params;
if(bc) check_per_bound(moldyn,&dist_jk);
d_jk=v3_norm(&dist_jk);
- beta=*(exchange->beta);
- betan=exchange->betan;
+ /* get exchange data */
n=*(exchange->n);
c=*(exchange->c);
d=*(exchange->d);
h=*(exchange->h);
- chi=exchange->chi;
c2=exchange->c2;
d2=exchange->d2;
c2d2=exchange->c2d2;
numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
denom=2*d_ij*d_ik;
cos_theta=numer/denom;
+ /* prefere law of cosines, dot product -> nan (often) */
//cos_theta=v3_scalar_product(&dist_ij,&dist_ik)/(d_ij*d_ik);
sin_theta=sqrt(1.0-(cos_theta*cos_theta));
theta=acos(cos_theta);
d_theta2*=d_theta;
h_cos=(h-cos_theta);
- h_cos2=h_cos*h_cos;
- d2_h_cos2=d2+h_cos2;
+ d2_h_cos2=d2+(h_cos*h_cos);
+
+ frac=c2/(d2_h_cos2);
+ g=1.0+c2d2-frac;
- /* some usefull expressions */
- frac1=c2/(d2_h_cos2);
- bracket1=1+c2d2-frac1;
if(f_c_ik==0.0) {
- bracket2=0.0;
- bracket2_n_1=0.0;
- bracket2_n=0.0;
- bracket3=1.0;
- printf("Foo -> 0: ");
+ bracket=0.0;
+ bracket_n_1=0.0;
+ bracket_n=0.0;
+ //printf("Foo -> 0: ");
}
else {
- bracket2=f_c_ik*bracket1;
- bracket2_n_1=pow(bracket2,n-1.0);
- bracket2_n=bracket2_n_1*bracket2;
- bracket3=1.0+betan*bracket2_n;
- printf("Foo -> 1: ");
+ bracket=f_c_ik*g;
+ bracket_n_1=pow(bracket,n-1.0);
+ bracket_n=bracket_n_1*bracket;
+ //printf("Foo -> 1: ");
}
- bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
- bracket3_pow=bracket3_pow_1*bracket3;
-printf("%.15f %.15f %.15f\n",bracket2_n_1,bracket2_n);
+//printf("%.15f %.15f %.15f\n",bracket_n_1,bracket_n,bracket);
- /* now go on with calc of b_ij and derivation of b_ij */
- b_ij=chi*bracket3_pow;
+ /* calc of db_ij and the 2 sums */
+ exchange->sum1_3bp+=bracket_n;
+ exchange->sum2_3bp+=bracket_n_1;
/* derivation of theta */
v3_scale(&force,&dist_ij,d_theta1);
v3_scale(&temp,&dist_ik,d_theta2);
v3_add(&force,&force,&temp);
- /* part 1 of derivation of b_ij */
- v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
+ /* part 1 of db_ij */
+ v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac/d2_h_cos2);
- /* part 2 of derivation of b_ij */
- v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
+ /* part 2 of db_ij */
+ v3_scale(&temp,&dist_ik,df_c_ik*g);
- /* sum up and scale ... */
+ /* sum up and add to db_ij */
v3_add(&temp,&temp,&force);
- scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
- v3_scale(&temp,&temp,scale);
-
- /* now construct an energy and a force out of that */
- v3_scale(&temp,&temp,f_a);
- v3_scale(&force,&dist_ij,df_a*b_ij);
- v3_add(&temp,&temp,&force);
- v3_scale(&temp,&temp,f_c);
- v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
- v3_add(&force,&force,&temp);
-
- /* add forces */
- v3_add(&(ai->f),&(ai->f),&force);
- /* energy is 0.5 f_r f_c */
- moldyn->energy+=(0.5*f_a*b_ij*f_c);
+ v3_add(&(exchange->db_ij),&(exchange->db_ij),&temp);
return 0;
}
projects / physik / posic.git / blobdiff